Hi Roni, you can probably rename the as.data.frame in $SPARK_HOME/R/pkg/R/DataFrame.R and re-install SparkR by running install-dev.sh
On Tue, Mar 15, 2016 at 8:46 AM, roni <roni.epi...@gmail.com> wrote: > Hi , > Is there a work around for this? > Do i need to file a bug for this? > Thanks > -R > > On Tue, Mar 15, 2016 at 12:28 AM, Sun, Rui <rui....@intel.com> wrote: > >> It seems as.data.frame() defined in SparkR convers the versions in R base >> package. >> >> We can try to see if we can change the implementation of as.data.frame() >> in SparkR to avoid such covering. >> >> >> >> *From:* Alex Kozlov [mailto:ale...@gmail.com] >> *Sent:* Tuesday, March 15, 2016 2:59 PM >> *To:* roni <roni.epi...@gmail.com> >> *Cc:* user@spark.apache.org >> *Subject:* Re: sparkR issues ? >> >> >> >> This seems to be a very unfortunate name collision. SparkR defines it's >> own DataFrame class which shadows what seems to be your own definition. >> >> >> >> Is DataFrame something you define? Can you rename it? >> >> >> >> On Mon, Mar 14, 2016 at 10:44 PM, roni <roni.epi...@gmail.com> wrote: >> >> Hi, >> >> I am working with bioinformatics and trying to convert some scripts to >> sparkR to fit into other spark jobs. >> >> >> >> I tries a simple example from a bioinf lib and as soon as I start sparkR >> environment it does not work. >> >> >> >> code as follows - >> >> countData <- matrix(1:100,ncol=4) >> >> condition <- factor(c("A","A","B","B")) >> >> dds <- DESeqDataSetFromMatrix(countData, DataFrame(condition), ~ >> condition) >> >> >> >> Works if i dont initialize the sparkR environment. >> >> if I do library(SparkR) and sqlContext <- sparkRSQL.init(sc) it gives >> following error >> >> >> >> > dds <- DESeqDataSetFromMatrix(countData, as.data.frame(condition), ~ >> condition) >> >> Error in DataFrame(colData, row.names = rownames(colData)) : >> >> cannot coerce class "data.frame" to a DataFrame >> >> >> >> I am really stumped. I am not using any spark function , so i would >> expect it to work as a simple R code. >> >> why it does not work? >> >> >> >> Appreciate the help >> >> -R >> >> >> >> >> >> >> >> -- >> >> Alex Kozlov >> (408) 507-4987 >> (650) 887-2135 efax >> ale...@gmail.com >> > > -- Alex Kozlov (408) 507-4987 (650) 887-2135 efax ale...@gmail.com
